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Capoferri D, Chiodelli P, Corli M, Belleri M, Scalvini E, Mignani L, Guerra J, Grillo E, De Giorgis V, Manfredi M, Presta M. The Pro-Oncogenic Sphingolipid-Metabolizing Enzyme β-Galactosylceramidase Modulates the Proteomic Landscape in BRAF(V600E)-Mutated Human Melanoma Cells. Int J Mol Sci 2023; 24:10555. [PMID: 37445731 DOI: 10.3390/ijms241310555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
β-Galactosylceramidase (GALC) is a lysosomal enzyme involved in sphingolipid metabolism by removing β-galactosyl moieties from β-galactosylceramide and β-galactosylsphingosine. Previous observations have shown that GALC may exert pro-oncogenic functions in melanoma and Galc silencing, leading to decreased oncogenic activity in murine B16 melanoma cells. The tumor-driving BRAF(V600E) mutation is present in approximately 50% of human melanomas and represents a major therapeutic target. However, such mutation is missing in melanoma B16 cells. Thus, to assess the impact of GALC in human melanoma in a more relevant BRAF-mutated background, we investigated the effect of GALC overexpression on the proteomic landscape of A2058 and A375 human melanoma cells harboring the BRAF(V600E) mutation. The results obtained by liquid chromatography-tandem mass spectrometry (LC-MS/MS) demonstrate that significant differences exist in the protein landscape expressed under identical cell culture conditions by A2058 and A375 human melanoma cells, both harboring the same BRAF(V600E)-activating mutation. GALC overexpression resulted in a stronger impact on the proteomic profile of A375 cells when compared to A2058 cells (261 upregulated and 184 downregulated proteins versus 36 and 14 proteins for the two cell types, respectively). Among them, 25 proteins appeared to be upregulated in both A2058-upGALC and A375-upGALC cells, whereas two proteins were significantly downregulated in both GALC-overexpressing cell types. These proteins appear to be involved in melanoma biology, tumor invasion and metastatic dissemination, tumor immune escape, mitochondrial antioxidant activity, endoplasmic reticulum stress responses, autophagy, and/or apoptosis. Notably, analysis of the expression of the corresponding genes in human skin cutaneous melanoma samples (TCGA, Firehose Legacy) using the cBioPortal for Cancer Genomics platform demonstrated a positive correlation between GALC expression and the expression levels of 14 out of the 27 genes investigated, thus supporting the proteomic findings. Overall, these data indicate for the first time that the expression of the lysosomal sphingolipid-metabolizing enzyme GALC may exert a pro-oncogenic impact on the proteomic landscape in BRAF-mutated human melanoma.
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Affiliation(s)
- Davide Capoferri
- Unit of Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Paola Chiodelli
- Unit of Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Marzia Corli
- Unit of Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Mirella Belleri
- Unit of Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Elisa Scalvini
- Unit of Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Luca Mignani
- Unit of Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Jessica Guerra
- Unit of Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Elisabetta Grillo
- Unit of Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Veronica De Giorgis
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy
- Center for Allergic and Autoimmune Diseases, University of Piemonte Orientale, 28100 Novara, Italy
| | - Marcello Manfredi
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy
- Center for Allergic and Autoimmune Diseases, University of Piemonte Orientale, 28100 Novara, Italy
| | - Marco Presta
- Unit of Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
- Consorzio Interuniversitario Biotecnologie (CIB), Unit of Brescia, 25123 Brescia, Italy
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Ou L, Liu S, Wang H, Guo Y, Guan L, Shen L, Luo R, Elder DE, Huang AC, Karakousis G, Miura J, Mitchell T, Schuchter L, Amaravadi R, Flowers A, Mou H, Yi F, Guo W, Ko J, Chen Q, Tian B, Herlyn M, Xu X. Patient-derived melanoma organoid models facilitate the assessment of immunotherapies. EBioMedicine 2023; 92:104614. [PMID: 37229906 PMCID: PMC10277922 DOI: 10.1016/j.ebiom.2023.104614] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND Only a minority of melanoma patients experience durable responses to immunotherapies due to inter- and intra-tumoral heterogeneity in melanoma. As a result, there is a pressing need for suitable preclinical models to investigate resistance mechanisms and enhance treatment efficacy. METHODS Here, we report two different methods for generating melanoma patient-derived organoids (MPDOs), one is embedded in collagen gel, and the other is inlaid in Matrigel. MPDOs in Matrigel are used for assessing the therapeutic effects of anti-PD-1 antibodies (αPD-1), autochthonous tumor infiltrating lymphocytes (TILs), and small molecule compounds. MPDOs in collagen gel are used for evaluating the chemotaxis and migratory capacity of TILs. FINDING The MPDOs in collagen gel and Matrigel have similar morphology and immune cell composition to their parental melanoma tissues. MPDOs show inter- and intra-tumoral heterogeneity and contain diverse immune cells such as CD4+, CD8+ T, Treg, CD14+ monocytic, CD15+, and CD11b+ myeloid cells. The tumor microenvironment (TME) in MPDOs is highly immunosuppressive, and the lymphoid and myeloid lineages express similar levels of PD-1, PD-L1, and CTLA-4 as their parental melanoma tissues. Anti-PD-1 antibodies (αPD-1) reinvigorate CD8+ T cells and induce melanoma cell death in the MPDOs. TILs expanded by IL-2 and αPD-1 show significantly lower expression of TIM-3, better migratory capacity and infiltration of autochthonous MPDOs, and more effective killing of melanoma cells than TILs expanded by IL-2 alone or IL-2 with αCD3. A small molecule screen discovers that Navitoclax increases the cytotoxicity of TIL therapy. INTERPRETATION MPDOs may be used to test immune checkpoint inhibitors and cellular and targeted therapies. FUNDING This work was supported by the NIH grants CA114046, CA261608, CA258113, and the Tara Miller Melanoma Foundation.
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Affiliation(s)
- Lingling Ou
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA; Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, China
| | - Shujing Liu
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Huaishan Wang
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yeye Guo
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lei Guan
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Longbin Shen
- The First Affiliated Hospital of Jinan University, Guangzhou, 510632, China
| | - Ruhui Luo
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, China
| | - David E Elder
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Alexander C Huang
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Giorgos Karakousis
- Department of Surgery, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - John Miura
- Department of Surgery, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Tara Mitchell
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lynn Schuchter
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ravi Amaravadi
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ahron Flowers
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Haiwei Mou
- The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Fan Yi
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Wei Guo
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jina Ko
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Qing Chen
- The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Bin Tian
- The Wistar Institute, Philadelphia, PA, 19104, USA
| | | | - Xiaowei Xu
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Azimi A, Patrick E, Teh R, Kim J, Fernandez-Penas P. Proteomic profiling of cutaneous melanoma explains the aggressiveness of distant organ metastasis. Exp Dermatol 2023. [PMID: 37082900 DOI: 10.1111/exd.14814] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 04/22/2023]
Abstract
Despite recent developments in managing metastatic melanomas, patients' overall survival remains low. Therefore, the current study aims to understand better the proteome-wide changes associated with melanoma metastasis that will assist with identifying targeted therapies. The latest development in mass spectrometry-based proteomics, together with extensive bioinformatics analysis, was used to investigate the molecular changes in 60 formalin-fixed and paraffin-embedded samples of primary and lymph nodes (LN) and distant organ metastatic melanomas. A total of 4631 proteins were identified, of which 72 and 453 were significantly changed between the LN and distant organ metastatic melanomas compared to the primary lesions (adj. p-value <0.05). An increase in proteins such as SLC9A3R1, CD20 and GRB2 and a decrease in CST6, SERPINB5 and ARG1 were associated with regional LN metastasis. By contrast, increased metastatic activities in distant organ metastatic melanomas were related to higher levels of CEACAM1, MC1R, AKT1 and MMP3-9 and decreased levels of CDKN2A, SDC1 and SDC4 proteins. Furthermore, machine learning analysis classified the lesions with up to 92% accuracy based on their metastatic status. The findings from this study provide up to date proteome-level information about the progression of melanomas to regional LN and distant organs, leading to the identification of protein signatures with potential for clinical translation.
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Affiliation(s)
- Ali Azimi
- Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
- Department of Dermatology, Westmead Hospital, Westmead, New South Wales, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, Australia
| | - Ellis Patrick
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, Australia
- School of Mathematics and Statistics, Faculty of Science, The University of Sydney, Camperdown, New South Wales, Australia
- Sydney Precision Data Science Centre, The University of Sydney, Camperdown, New South Wales, Australia
| | - Rachel Teh
- Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
- Department of Dermatology, Westmead Hospital, Westmead, New South Wales, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, Australia
| | - Jennifer Kim
- Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, Australia
- Department of Tissue Pathology and Diagnostic Oncology, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia
| | - Pablo Fernandez-Penas
- Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
- Department of Dermatology, Westmead Hospital, Westmead, New South Wales, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, Australia
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Militaru IV, Rus AA, Munteanu CV, Manica G, Petrescu SM. New panel of biomarkers to discriminate between amelanotic and melanotic metastatic melanoma. Front Oncol 2023; 12:1061832. [PMID: 36776379 PMCID: PMC9909407 DOI: 10.3389/fonc.2022.1061832] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/28/2022] [Indexed: 01/27/2023] Open
Abstract
Melanoma is a form of skin cancer that can rapidly invade distant organs. A distinctive feature of melanomas is their pigmentation status, as melanin is present in most skin melanomas, whilst many metastatic tumors could become amelanotic. Besides the obvious malfunction of the key genes of the melanin pathway, the amelanotic tumors could bear a characteristic molecular signature accounting for their aggressivity. Using mass spectrometry-based proteomics we report here a distinctive panel of biomarkers for amelanotic aggressive melanoma that differ from the less invasive pigmented cells. The developed method allows the label-free quantification of proteins identified by LC-MS/MS analysis. We found a set of proteins comprising AHNAK, MYOF, ANXA1, CAPN2, ASPH, EPHA2, THBS1, TGM2, ACTN4 along with proteins involved in cell adhesion/migration (integrins, PLEC, FSCN1, FN1) that are highly expressed in amelanotic melanoma. Accompanying the down regulation of pigmentation specific proteins such as tyrosinase and TYRP1, these biomarkers are highly specific for a type of highly invasive melanoma. Interestingly, the LC-MS/MS proteomics analysis in hypoxia revealed that the abundance of this specific set of proteins found in normoxia was rather unaltered in these conditions. These biomarkers could therefore predict a metastatic behaviour for the amelanotic cells in the early stages of the tumor development and thus serve in melanoma prognostic. Applying this algorithm to related databases including melanoma samples published by independent laboratories/public databases we confirm the specificity of the newly found signatures. Overall, we begin to unravel the molecular alterations in the amelanotic melanoma and how basic proteomics offers insights into how to assess the clinical, pathological and misdiagnosis differences between the main subtypes of melanoma.
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Affiliation(s)
- Ioana V. Militaru
- Department of Molecular Cell Biology, Institute of Biochemistry, Bucharest, Romania
| | - Alina Adriana Rus
- Department of Molecular Cell Biology, Institute of Biochemistry, Bucharest, Romania
| | - Cristian V.A. Munteanu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry, Bucharest, Romania
| | - Georgiana Manica
- Department of Molecular Cell Biology, Institute of Biochemistry, Bucharest, Romania
| | - Stefana M. Petrescu
- Department of Molecular Cell Biology, Institute of Biochemistry, Bucharest, Romania,*Correspondence: Stefana M. Petrescu,
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Dawood S, Ali ZJ. Entrectinib for NTRK Fusion-Positive Metastatic Melanoma Progressing on Combined PD-1 and CTLA-4 Inhibition: A Case Report. Case Rep Oncol 2023; 16:1451-1459. [PMID: 38028569 PMCID: PMC10673342 DOI: 10.1159/000534475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 10/03/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction The burden of melanoma is increasing globally. Despite the use of immunotherapy and targeted therapy, the prognosis of metastatic melanoma remains relatively poor. The integration of comprehensive molecular profiling can lead to the detection of actionable biomarkers and the expansion of treatment options, thereby prolonging cancer patient survival. Case Presentation We herein present the case of a female 54-year-old patient diagnosed with melanoma of the right knee, for which she underwent surgery. Patient showed progression of disease after 10 cycles of adjuvant nivolumab. Ipilimumab (1 mg/kg every 3 weeks) was added to the treatment regimen but no clinical improvement was observed. Molecular profiling was conducted based on patient tissue, and an ANXA2-NTRK3 fusion was detected in the tumor. This specific fusion has not been previously reported; however, it is in-frame and similar to other known oncogenic NTRK fusions. At the time of entrectinib initiation, the patient had clear disease progression on the right leg on standard of care immunotherapy. She was commenced on entrectinib 200 mg once daily for 2 weeks. Dose escalation was attempted, and treatment intensity was managed based on drug tolerability. Good treatment response was observed on laboratory and radiologic parameters. As of September 2023, i.e., 2.5 years after treatment initiation, patient disease continues to be controlled with entrectinib. Conclusion Profiling of advanced tumors is important to determine the presence of agnostic markers that can be targeted and ultimately improve the prognostic outcome of patients after the failure of standard of care.
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Affiliation(s)
- Shaheenah Dawood
- Adjunct Clinical Professor, Mohammed Bin Rashid University of Medicine and Health Sciences, Consultant Medical Oncologist, Dubai, UAE
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Awah CU, Chen L, Bansal M, Mahajan A, Winter J, Lad M, Warnke L, Gonzalez-Buendia E, Park C, Zhang D, Feldstein E, Yu D, Zannikou M, Balyasnikova IV, Martuscello R, Konerman S, Győrffy B, Burdett KB, Scholtens DM, Stupp R, Ahmed A, Hsu P, Sonabend AM. Ribosomal protein S11 influences glioma response to TOP2 poisons. Oncogene 2020; 39:5068-5081. [PMID: 32528131 PMCID: PMC7646677 DOI: 10.1038/s41388-020-1342-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 05/22/2020] [Accepted: 05/29/2020] [Indexed: 12/26/2022]
Abstract
Topoisomerase II poisons are one of the most common class of chemotherapeutics used in cancer. We and others had shown that a subset of glioblastomas (GBM), the most malignant of all primary brain tumors in adults, are responsive to TOP2 poisons. To identify genes that confer susceptibility to this drug in gliomas, we performed a genome-scale CRISPR knockout screen with etoposide. Genes involved in protein synthesis and DNA damage were implicated in etoposide susceptibility. To define potential biomarkers for TOP2 poisons, CRISPR hits were overlapped with genes whose expression correlates with susceptibility to this drug across glioma cell lines, revealing ribosomal protein subunit RPS11, 16, 18 as putative biomarkers for response to TOP2 poisons. Loss of RPS11 led to resistance to etoposide and doxorubicin and impaired the induction of pro-apoptotic gene APAF1 following treatment. The expression of these ribosomal subunits was also associated with susceptibility to TOP2 poisons across cell lines from gliomas and multiple other cancers.
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Affiliation(s)
- Chidiebere U Awah
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University , Chicago, IL, United States
| | - Li Chen
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University , Chicago, IL, United States
| | | | - Aayushi Mahajan
- Department of Neurological Surgery, Columbia University Medical Center, Columbia University, New York City, NY, USA
| | - Jan Winter
- Functional Genomics and Signaling, German Center for Cancer Research, Heidelberg, Germany
| | - Meeki Lad
- Mailman School of Public Health, Columbia University, New York City, NY, USA
| | - Louisa Warnke
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University , Chicago, IL, United States
| | - Edgar Gonzalez-Buendia
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University , Chicago, IL, United States
| | - Cheol Park
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University , Chicago, IL, United States
| | - Daniel Zhang
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University , Chicago, IL, United States
| | - Eric Feldstein
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University , Chicago, IL, United States
| | - Dou Yu
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University , Chicago, IL, United States
| | - Markella Zannikou
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University , Chicago, IL, United States
| | - Irina V Balyasnikova
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University , Chicago, IL, United States
| | - Regina Martuscello
- Department of Pathology, Columbia University Medical Centre, Columbia University, New York City, NY, USA
| | | | - Balázs Győrffy
- MTA TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary.,2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Kirsten B Burdett
- Department of Preventive Medicine, Northwestern University, Chicago, IL, USA
| | - Denise M Scholtens
- Department of Preventive Medicine, Northwestern University, Chicago, IL, USA
| | - Roger Stupp
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University , Chicago, IL, United States
| | - Atique Ahmed
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University , Chicago, IL, United States
| | - Patrick Hsu
- Molecular and Cell Biology, Salk Institute, La Jolla, CA, USA
| | - Adam M Sonabend
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University , Chicago, IL, United States.
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